Itunes only syncs a fraction of music to Ipod

A few days ago, I noticed that both Safari and YouTube had mysteriously disappeared from my iPod Touch (32GB, 2G). I don't recall ever getting any type of error message and was completely unable from figuring out a way of getting them back on. I finally decided to restore my iPod to the original factory settings and after it was done restoring, both Safari and YouTube were back. Mission accomplished. However, when I went to sync all of my music and apps back onto my iPod, I discovered that only 1.69 GB of 11.28 GB of my music had actually synced. When the sync was over, however, I did get an error message saying certain songs had not been transferred since they could not be found (despite the fact that they are in my iTunes library), and it comes out to a total of 100 songs that can not be transferred. My movies, tv shows, podcasts, and apps all transferred just fine. I've never encountered this problem before and I'm running the most recent version of iTunes and iPod 3.0. Suggestions?